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- PDB-4fvd: Crystal structure of EV71 2A proteinase C110A mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 4fvd
TitleCrystal structure of EV71 2A proteinase C110A mutant in complex with substrate
Components
  • 10-mer peptide from 2A proteinase
  • 2A proteinasePicornain 2A
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / HYDROLASE / CYSTEINE PROTEINASE / HYDROLASE-HYDROLASE SUBSTRATE complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsCai, Q. / Muhammad, Y. / Liu, W. / Gao, Z. / Peng, X. / Cai, Y. / Wu, C. / Zheng, Q. / Li, J. / Lin, T.
CitationJournal: J.Virol. / Year: 2013
Title: Conformational Plasticity of 2A Proteinase from Enterovirus 71
Authors: Cai, Q. / Yameen, M. / Liu, W. / Gao, Z. / Li, Y. / Peng, X. / Cai, Y. / Wu, C. / Zheng, Q. / Li, J. / Lin, T.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2A proteinase
C: 10-mer peptide from 2A proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7533
Polymers17,6882
Non-polymers651
Water2,396133
1
A: 2A proteinase
C: 10-mer peptide from 2A proteinase
hetero molecules

A: 2A proteinase
C: 10-mer peptide from 2A proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5066
Polymers35,3754
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)86.566, 43.991, 51.764
Angle α, β, γ (deg.)90.000, 112.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

#1: Protein 2A proteinase / Picornain 2A


Mass: 16706.549 Da / Num. of mol.: 1 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Strain: E2004104-TW-CDC / Gene: polyprotein / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A9XG43, picornain 2A
#2: Protein/peptide 10-mer peptide from 2A proteinase


Mass: 981.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Strain: E2004104-TW-CDC / Gene: polyprotein / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A9XG43
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 20% 2-propanol, 10% PEG 4000, pH 7.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 21456 / Num. obs: 20028 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.66 % / Rmerge(I) obs: 0.0386 / Net I/σ(I): 11.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.4443 / Mean I/σ(I) obs: 1.2 / % possible all: 78.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FVB

4fvb


Resolution: 1.66→40.07 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.993 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1032 5.2 %RANDOM
Rwork0.1895 ---
all0.1914 21456 --
obs0.1914 20028 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 27.4618 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.66→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 1 133 1226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211124
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9251530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43922.96354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.119159
X-RAY DIFFRACTIONr_chiral_restr0.1550.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021880
X-RAY DIFFRACTIONr_mcbond_it1.521.5701
X-RAY DIFFRACTIONr_mcangle_it2.56721119
X-RAY DIFFRACTIONr_scbond_it3.6573423
X-RAY DIFFRACTIONr_scangle_it5.2764.5410
LS refinement shellResolution: 1.661→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 69 -
Rwork0.402 1249 -
all-1318 -
obs--83.79 %

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